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#include <algorithm> |
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#include <cstdlib> |
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#include <stdlib.h> |
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#include <iostream> |
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#include <cmath> |
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#include <math.h> |
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#include <string> |
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#include <sprng.h> |
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTxyz_ENS 4 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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using namespace std; |
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|
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SimSetup::SimSetup(){ |
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|
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initSuspend = false; |
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isInfoArray = 0; |
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nInfo = 1; |
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|
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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initSuspend = true; |
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} |
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#endif // is_mpi |
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void SimSetup::createSim(void){ |
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int i, j, k, globalAtomIndex; |
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|
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// gather all of the information from the Bass file |
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sysObjectsCreation(); |
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// check on the post processing info |
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|
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finalInfoCheck(); |
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|
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// initialize the system coordinates |
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|
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if (!isInfoArray){ |
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if ( !initSuspend ){ |
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initSystemCoords(); |
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|
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if( !(globals->getUseInitTime()) ) |
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info[0].currentTime = 0.0; |
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} |
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|
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// check on the post processing info |
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|
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finalInfoCheck(); |
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|
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// make the output filenames |
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makeOutNames(); |
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|
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void SimSetup::makeMolecules(void){ |
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int k, l; |
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int k; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
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void SimSetup::gatherInfo(void){ |
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int i, j, k; |
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int i; |
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|
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ensembleCase = -1; |
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ffCase = -1; |
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else if (!strcasecmp(ensemble, "NPTf")){ |
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ensembleCase = NPTf_ENS; |
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} |
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else if (!strcasecmp(ensemble, "NPTxyz")){ |
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ensembleCase = NPTxyz_ENS; |
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} |
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup Warning. Unrecognized Ensemble -> %s, " |
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} |
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|
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// check for the temperature set flag |
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|
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|
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if (globals->haveTempSet()) |
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info[i].setTemp = globals->getTempSet(); |
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|
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// get some of the tricky things that may still be in the globals |
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|
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double boxVector[3]; |
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if (globals->haveBox()){ |
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boxVector[0] = globals->getBox(); |
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boxVector[1] = globals->getBox(); |
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boxVector[2] = globals->getBox(); |
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// check for the extended State init |
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|
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info[i].setBox(boxVector); |
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} |
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else if (globals->haveDensity()){ |
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double vol; |
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vol = (double) tot_nmol / globals->getDensity(); |
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boxVector[0] = pow(vol, (1.0 / 3.0)); |
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boxVector[1] = boxVector[0]; |
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boxVector[2] = boxVector[0]; |
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|
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info[i].setBox(boxVector); |
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} |
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else{ |
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if (!globals->haveBoxX()){ |
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sprintf(painCave.errMsg, |
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"SimSetup error, no periodic BoxX size given.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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boxVector[0] = globals->getBoxX(); |
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|
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if (!globals->haveBoxY()){ |
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sprintf(painCave.errMsg, |
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"SimSetup error, no periodic BoxY size given.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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boxVector[1] = globals->getBoxY(); |
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|
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if (!globals->haveBoxZ()){ |
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sprintf(painCave.errMsg, |
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"SimSetup error, no periodic BoxZ size given.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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boxVector[2] = globals->getBoxZ(); |
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|
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info[i].setBox(boxVector); |
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} |
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info[i].useInitXSstate = globals->getUseInitXSstate(); |
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info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
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|
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} |
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|
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|
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//setup seed for random number generator |
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int seedValue; |
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theEst = globals->getEST(); |
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} |
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info[i].setEcr(theEcr, theEst); |
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info[i].setDefaultEcr(theEcr, theEst); |
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|
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if (!globals->haveDielectric()){ |
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sprintf(painCave.errMsg, |
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theEst = globals->getEST(); |
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} |
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info[i].setEcr(theEcr, theEst); |
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info[i].setDefaultEcr(theEcr, theEst); |
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} |
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} |
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|
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if( !initSuspend ) |
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info[i].checkCutOffs(); |
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} |
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#ifdef IS_MPI |
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if (worldRank == 0){ |
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#endif //is_mpi |
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inName = globals->getInitialConfig(); |
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double* tempDouble = new double[1000000]; |
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fileInit = new InitializeFromFile(inName); |
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#ifdef IS_MPI |
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} |
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|
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sprintf(painCave.errMsg, |
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"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
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painCave.isFatal; |
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painCave.isFatal = 1;; |
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simError(); |
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|
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#else |
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} |
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void SimSetup::calcSysValues(void){ |
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int i, j, k; |
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int i; |
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int* molMembershipArray; |
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void SimSetup::makeSysArrays(void){ |
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int i, j, k, l; |
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|
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#ifndef IS_MPI |
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int k, j; |
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#endif // is_mpi |
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int i, l; |
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|
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Atom** the_atoms; |
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Molecule* the_molecules; |
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NVT<RealIntegrator>* myNVT = NULL; |
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NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
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NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
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NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
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|
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for (k = 0; k < nInfo; k++){ |
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switch (ensembleCase){ |
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|
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if (globals->haveTauThermostat()) |
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myNPTf->setTauThermostat(globals->getTauThermostat()); |
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|
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
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|
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if (globals->haveTauBarostat()) |
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myNPTf->setTauBarostat(globals->getTauBarostat()); |
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|
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
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} |
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|
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info->the_integrator = myNPTf; |
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break; |
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|
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case NPTxyz_ENS: |
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if (globals->haveZconstraints()){ |
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setupZConstraint(info[k]); |
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myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
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} |
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else |
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myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
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|
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myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
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|
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if (globals->haveTargetPressure()) |
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myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error: If you use a constant pressure\n" |
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" ensemble, you must set targetPressure in the BASS file.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
1467 |
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|
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if (globals->haveTauThermostat()) |
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myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
1473 |
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" ensemble, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
1475 |
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simError(); |
1476 |
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} |
1477 |
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|
1478 |
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if (globals->haveTauBarostat()) |
1479 |
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myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1480 |
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else{ |
1481 |
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sprintf(painCave.errMsg, |
1482 |
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"SimSetup error: If you use an NPT\n" |
1483 |
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" ensemble, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
1485 |
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simError(); |
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} |
1487 |
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|
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info->the_integrator = myNPTxyz; |
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break; |
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|
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default: |